Hi,
I would also love to know what fixed it! I have the same noise when the engine is hot and clutch lever pulled in. (I have my brother's old 2002 R1150 GSA with 90,000 km on it).
I installed a second hand gearbox as the old one had stripped splines on the input shaft. Put in a new clutch as well but the noise is still there. Also put in the LHS ugrade cam chain tensioner. The bike runs really well, but that noise sure sounds awful!
From looking at heaps of other posts it seems it is fairly common - one idea is that is the crankshaft thrust bearing can wear when overheated (which I think ocurred when the bike was ridden up north (of Western Australia) in summer). With the clutch engaged (lever out) when in neutral the clutch and tranmission stabilise the crankshaft but when disengaged (lever in) the crankshaft is free to move back and forth within its end play. That's the theory proposed by people who know more than me anyway!
However, if the OP's noise has gone, it would be so good to find out what fixed it!
Cheers
Chris